# ToxCast Data Analysis Pipeline

## Documentation for package ‘tcpl’ version 3.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C F H I L M Q R S T W misc

## -- B --

blineShift | Shift the baseline to 0

## -- C --

chdat | Chemical library of tested chemicals in the example datasets with the corresponding sample IDs.
check_tcpl_db_schema | Function that checks if the most recent v3 table schema is used in the database schema
Configure functions | Functions for configuring the tcpl package

## -- F --

flareFunc | Calculate the weighted mean of a square to detect plate flares

## -- H --

Hill model utilites | Functions to solve the Hill model

## -- I --

interlaceFunc | Calculate the weighted mean of a square to detect interlace effect
invitrodb_dd | Short descriptions of fields for different tables are stored in a data dictionary.
is.odd | Check for odd numbers

## -- L --

Load assay information | Functions for loading assay information
lu | Abbreviation for 'length(unique(x))'
lw | Abbreviation for 'length(which(x))'

## -- M --

mc1 | Perform level 1 multiple-concentration processing
mc2 | Perform level 2 multiple-concentration processing
MC2_Methods | List of level 2 multiple-concentration correction functions
mc2_mthds | List of level 2 multiple-concentration correction functions
mc3 | Perform level 3 multiple-concentration processing
MC3_Methods | List of level 3 multiple-concentration normalization methods
mc3_mthds | List of level 3 multiple-concentration normalization methods
mc4 | Perform level 4 multiple-concentration processing
MC4_Methods | List of level 4 multiple-concentration methods for calculating bmad
mc4_mthds | List of level 4 multiple-concentration methods for calculating bmad
mc5 | Perform level 5 multiple-concentration processing
MC5_Methods | Load list of level 5 multiple-concentration cutoff methods
mc5_mthds | Load list of level 5 multiple-concentration cutoff methods
mc6 | Perform level 6 multiple-concentration processing
MC6_Methods | Load list of level 6 multiple-concentration flag methods
mc6_mthds | Load list of level 6 multiple-concentration flag methods
mcdat | A subset of ToxCast data showing changes in the activity of the intracellular estrogen receptor.
mc_vignette | List with multi-concentration data for the vignette
Method functions | Functions for managing processing methods
Models | Model objective functions

## -- Q --

Query functions | Wrappers for sending queries and fetching results

## -- R --

Register/update annotation | Functions for registering & updating annotation information
registerMthd | Add a new analysis method

## -- S --

sc1 | Perform level 1 single-concentration processing
SC1_Methods | List of level 1 single-concentration normalization functions
sc1_mthds | List of level 1 single-concentration normalization functions
sc2 | Perform level 2 single-concentration processing
SC2_Methods | List of level 2 single-concentration hit-call functions
sc2_mthds | List of level 2 single-concentration hit-call functions
scdat | A subset of ToxCast data showing changes in transcription factor activity for multiple targets.
sc_vignette | List with single-concentration data for the vignette
sink.reset | Reset all sinks

## -- T --

tcplAddModel | Draw a tcpl Model onto an existing plot
tcplAICProb | Calculate the AIC probabilities
tcplAppend | Append rows to a table
tcplCascade | Do a cascading delete on tcpl screening data
tcplCode2CASN | Convert chemical code to CAS Registry Number
tcplConf | Functions for configuring the tcpl package
tcplConfDefault | Functions for configuring the tcpl package
tcplConfExample | Functions for configuring the tcpl package
tcplConfList | Functions for configuring the tcpl package
tcplConfLoad | Functions for configuring the tcpl package
tcplConfReset | Functions for configuring the tcpl package
tcplConfSave | Functions for configuring the tcpl package
tcplCytoPt | Calculate the cytotoxicity point based on the "burst" endpoints
tcpldbStats | Get summary statistics for the database
tcplDefine | Load data dictionary descriptions
tcplDelete | Delete rows from tcpl databases
tcplFit | Fit the data with the constant, hill, and gain-loss models
tcplFit2 | tcpl Wrapper for tcplfit2_core including additional calculations to fit into new schema
tcplFit2_nest | Nest dataframe into a list that is readable by tcplfit2
tcplFit2_unnest | Unnest tcplfit2 parameters into a dataframe
tcplGetAeid | get Aeid for endpoint name
tcplggplot | tcplggplot
tcplHillACXX | Functions to solve the Hill model
tcplHillConc | Functions to solve the Hill model
tcplHillVal | Functions to solve the Hill model
tcplHit2 | Hitcalling with tcplfit2
tcplListFlds | Load the field names for a table
tcplLoadAcid | Functions for loading assay information
tcplLoadAeid | Functions for loading assay information
tcplLoadAid | Functions for loading assay information
tcplLoadAsid | Functions for loading assay information
tcplLoadChem | Load sample/chemical information
tcplLoadClib | Load chemical library information
tcplLoadConcUnit | Load concentration units for assay endpoints
tcplLoadData | Load tcpl data
tcplLoadUnit | Load response units for assay endpoints
tcplLvlCount | Load tcpl level counts
tcplMakeAeidMultiPlts | Create a .pdf with all dose-response plots for a given aeid, 6 per page
tcplMakeAeidPlts | Create a .pdf with dose-response plots
tcplMakeChidMultiPlts | Create a .pdf with all dose-response plots for a given chid, 6 per page
tcplMthdAssign | Functions for managing processing methods
tcplMthdClear | Functions for managing processing methods
tcplMthdList | Functions for managing processing methods
tcplMthdLoad | Functions for managing processing methods
tcplMultiplot | Plot summary fits based on fit and dose-response data
tcplObjCnst | Model objective functions
tcplObjGnls | Model objective functions
tcplObjHill | Model objective functions
tcplPlot | #--- Generic Plotting Function for tcpl
tcplPlotFitc | Plot the fit category tree
tcplPlotFits | Plot summary fits based on fit and dose-response data
tcplPlotlyPlot | tcplPlotlyPlot
tcplPlotM4ID | Plot fit summary plot by m4id
tcplPlotPlate | Plot plate heatmap
tcplPrepOtpt | Map assay/chemical ID values to annotation information
tcplQuery | Wrappers for sending queries and fetching results
tcplRegister | Functions for registering & updating annotation information
tcplRun | Perform data processing
tcplSendQuery | Wrappers for sending queries and fetching results
tcplSubsetChid | Subset level 5 data to a single sample per chemical
tcplUpdate | Functions for registering & updating annotation information
tcplVarMat | Create chemical by assay matrices
tcplWriteData | Write screening data into the tcpl databases
tcplWriteLvl0 | Write level 0 screening data into the tcpl databases

## -- W --

write_lvl_4 | Write level 4 with updated schema

## -- misc --

.buildAssayQ | Generate query for assay information
.convertNames | Convert assay names to their abbreviations
.load6DR | Load data for tcpl6
.plateHeat | Plot plate heatmap
.prepField | Paste appropriate table name to field name